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Old 08-02-2012, 12:01 AM   #2
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415

Obviously, I would recommend newbler from 454. However, there is also a program from the Broad specifically designed for your taks:

AV454 (AssembleViral454) is an assembler, based on the ARACHNE package, designed for small and non-repetitive genomes sequenced at high depth. It was specifically designed to assemble read data generated from a mixed population of viral genomes.
Found here.
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